People in Western Australia sheltering from a category four cyclone in the Pilbara are likely to be stuck inside for some time as the intense weather system, bringing destructive winds and dangerous flooding with it, makes its way across the region very slowly.

It's one of two duelling weather systems wreaking havoc on the east and west coasts of Australia.

People in the Pilbara from Pardoo to Whim Creek including Port Hedland and South Hedland, are on "red alert" as cyclone Rusty moves towards the area.

It is likely the alert will not be downgraded for some time and they may have to stay sheltered for up to 36 hours.

The Department of Fire and Emergency Services has urged people to be patient, saying the weather poses a threat to lives and homes.

The cyclone has brought strong winds to the area, despite still being off the coast, and will slowly move over the area, meaning highly dangerous winds and rain are expected to continue into Thursday.

Two relocation centres - one in Port Hedland and one in South Hedland - are reportedly close to capacity.

More than a dozen schools in the area are closed and hundreds of houses in the area were without power.

People in low lying areas of Port Hedland, were urged to relocate because of fears of a storm surge in the area.

This morning, Rusty was estimated to be 130 kilometres north-north-east of Port Hedland and 290 kilometres east-north-east of Karratha and near stationary.

Wind gusts to 120kmh have already been experienced in Port Hedland and winds exceeding 230kmh were likely to develop.

EAST COAST SWAMPED

On Australia's east coast, a number of central Queensland towns and hamlets have been isolated by floodwaters for the second time in two months after torrential rains.

Rusty's influence was being widely felt as it brought clouds and rain across the continent, reaching Victoria. "It's moisture streaming from Rusty," said Brett Dutschke, senior meteorologist at Weatherzone.

Combined with moisture coming off the Pacific, "it's the highest humidity we've seen this summer" across the country, forecasters said.

Rivers have broken their banks in the Banana, Gladstone and Fraser Coast regions of Queensland.

Banana Shire Mayor Ron Carrige said all roads leading to the town of Biloela were swamped by floodwaters.

''We're pretty well stranded at the moment,'' he told AAP.''We're cut off north, south, east and west.''

Some farmers had just started replanting after floods last month.

''I don't know how much more you can wreck things that are already wrecked,'' Carrige said.

And the council wasn't sure when the floodwaters would recede.

''I want to get home myself. All we can do is watch it and see,'' Carrige said.

Southeast of Bileola, Maryborough was preparing for the Mary River to peak at seven metres about 8am (10am NZT) on Thursday.